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arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor (+3 others)
2005 BMC Bioinformatics  
of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH).  ...  We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying  ...  Conclusion We present arrayCGHbase, a versatile web based, platform independent data storage and analysis tool for processing microarray CGH data.  ... 
doi:10.1186/1471-2105-6-124 pmid:15910681 pmcid:PMC1173083 fatcat:o23fqjhs2vafnfykt5w3hyif7e

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

Malte Mader, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
2011 Journal of Clinical Bioinformatics  
Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate.  ...  The FISH Oracle application and an installed demo web server are available at  ...  In the following we will use the term array CGH (array comparative genomic hybridization) as a synonym for methods generating copy number data including classical array CGH tiling microarrays or SNP microarrays  ... 
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

Array comparative genomic hybridization and flow cytometry analysis of spontaneous abortions and mors in utero samples

Björn Menten, Katrien Swerts, Barbara Delle Chiaie, Sandra Janssens, Karen Buysse, Jan Philippé, Frank Speleman
2009 BMC Medical Genetics  
For several decades chromosome analysis has been the golden standard to detect these genomic imbalances. A major drawback of this method is the requirement of short term cultures of fetal cells.  ...  Karyotyping was unsuccessful in 28% of cases as compared to only two out of hundred samples with inconclusive results for combined array CGH and FCM analysis.  ...  Acknowledgements We are grateful to the patients and their family for their cooperation. The authors wish to thank Ivy Jennes and Katrien Broekaert for expert technical assistance.  ... 
doi:10.1186/1471-2350-10-89 pmid:19751515 pmcid:PMC2753309 fatcat:hk6ucohrsndtzlwx6ykqoh3jga

CAPweb: a bioinformatics CGH array Analysis Platform

S. Liva, P. Hupe, P. Neuvial, I. Brito, E. Viara, P. L. Rosa, E. Barillot
2006 Nucleic Acids Research  
The recently developed array-CGH (comparative genomic hybridization) technology allows this to be investigated at the genomic level.  ...  CAPweb (CGH array Analysis Platform on the Web) is intended as a user-friendly tool enabling biologists to completely analyse CGH arrays from the raw data to the visualization and biological interpretation  ...  Funding to pay the Open Access publication charges for this article was provided by Institut Curie.  ... 
doi:10.1093/nar/gkl215 pmid:16845053 pmcid:PMC1538852 fatcat:zkirbuwc7nalldmovmbxc3has4

Low-grade chromosomal mosaicism in human somatic and embryonic stem cell populations

Kurt Jacobs, Afroditi Mertzanidou, Mieke Geens, Ha Thi Nguyen, Catherine Staessen, Claudia Spits
2014 Nature Communications  
Here we study the genetic content of 92 individual human cells, including fibroblasts, amniocytes and embryonic stem cells (hESCs), using single-cell array-based comparative genomic hybridization (aCGH  ...  The recent development of high-resolution full-genome analysis methods applicable to single cells is providing new insights into genetic and cellular diversity.  ...  Stem Cell Laboratory for the derivation and culture of the cell lines.  ... 
doi:10.1038/ncomms5227 pmid:24970340 fatcat:osgmsmhlijcppkgm24nb5yyjvq

CGHPRO -- a comprehensive data analysis tool for array CGH

Wei Chen, Fikret Erdogan, H-Hilger Ropers, Steffen Lenzner, Reinhard Ullmann
2005 BMC Bioinformatics  
Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances.  ...  We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data.  ...  , Sarah Shoichet for reading the manuscript, Martin Vingron for fruitful discussions and the anonymous reviewers for their helpful comments.  ... 
doi:10.1186/1471-2105-6-85 pmid:15807904 pmcid:PMC1274268 fatcat:dai7bg4zcffjjnnd6le5wsgtpi

Scientific Poster Presentations

2018 Innovations (Philadelphia): technology and techniques in cardiothoracic and vascular surgery  
Methods and Materials. cDNA microarray expression profiling with over 17,000 probes, and array comparative genomic hybridization (aCGH) on 1Mb-spaced or full genomic tiling path BAC platforms, were used  ...  Comparative genomic hybridization microarrays (array CGH or molecular karyotyping) for the detection of constitutional chromosomal aberrations is the application of microarray technology that is coming  ... 
doi:10.1097/imi.0000000000000475 pmid:29668500 fatcat:5nsrkts2obabzead6aqfueflva

Scientific Poster Presentations

2007 Cellular Oncology  
All samples contained >60% of tumour cells as assessed by pathological analysis. aCGH was performed in a 44K oligonucleotide Human Genome CGH Microarray platform from Agilent Technologies.  ...  We aimed to characterize new genomic alterations in primary melanocytic lesions by using a high resolution CGH array platform.  ...  Comparative genomic hybridization microarrays (array CGH or molecular karyotyping) for the detection of constitutional chromosomal aberrations is the application of microarray technology that is coming  ... 
doi:10.1155/2007/490242 doaj:bfd9d2a9659c4b6f94755e4d9ed1a380 fatcat:alhh6bfk6badjkr5hm6cc2vdsu

Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes

Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes Hubertus Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken (+10 others)
2013 PLoS ONE  
Next we applied an integrated genomics analysis to prioritize MYCN down regulated genes mediated by MYCN driven miRNAs within regions of focal heterozygous or homozygous deletion.  ...  Neuroblastoma is an embryonic tumor arising from immature sympathetic nervous system cells.  ...  Acknowledgments We would like to acknowledge Fanny De Vloed, Lies Vantomme, Justine Nuytens, Els De Smet, Anneleen Beckers, Jeroen Schacht, Kathleen Claes and Nathalie Goderis for their excellent technical  ... 
doi:10.1371/journal.pone.0052321 pmid:23308108 pmcid:PMC3537730 fatcat:3kswu6iimre3hhwtorqq3y3u6q

Human embryonic stem cells show low-grade microsatellite instability

H. T. Nguyen, C. Markouli, M. Geens, L. Barbe, K. Sermon, C. Spits
2014 Molecular human reproduction  
An exception is the situation termed microsatellite instability (MSI), in which microsatellite loci change in size (Boland et al., 1998) .  ...  Microsatellites are stretches of repetitive DNA sequence and are scattered throughout the human genome (Weber, 1990) .  ...  Acknowledgements The authors acknowledge their colleagues from the HESC laboratory for the derivation and culture of the cell lines.  ... 
doi:10.1093/molehr/gau059 pmid:25082980 fatcat:4lsxfua7wbarrixosqsmugmhbi

A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies

K Althoff, A Beckers, E Bell, M Nortmeyer, T Thor, A Sprüssel, S Lindner, K De Preter, A Florin, L C Heukamp, L Klein-Hitpass, K Astrahantseff (+6 others)
2014 Oncogene  
Array comparative genome hybridization showed that chromosomal aberrations in LSL-MYCN;Dbh-iCre tumors were syntenic to those observed in human neuroblastomas.  ...  expression and genomic make up.  ...  This work was supported by the National Genome Research Network of the German Ministry for Education and Research (NGFNplus grant #PKN-01GS0894-6 to JHS, AE and AS), the 7th framework European Union project  ... 
doi:10.1038/onc.2014.269 pmid:25174395 pmcid:PMC4487199 fatcat:akr2jcsh7be65bqcfpkpmhhqd4

The H3K27me3 demethylase UTX is a gender-specific tumor suppressor in T-cell acute lymphoblastic leukemia

Joni Van der Meulen, Viraj Sanghvi, Konstantinos Mavrakis, Kaat Durinck, Fang Fang, Filip Matthijssens, Pieter Rondou, Monica Rosen, Tim Pieters, Peter Vandenberghe, Eric Delabesse, Tim Lammens (+11 others)
2014 Blood  
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive form of leukemia that is mainly diagnosed in children and shows a skewed gender distribution toward males.  ...  Interestingly, UTX mutations were exclusively present in male T-ALL patients and allelic expression analysis revealed that UTX escapes X-inactivation in female T-ALL lymphoblasts and normal T cells.  ...  and Research Animal Resource Center for assistance with mouse experiments, and the Laboratory of Comparative Pathology for histologic analysis.  ... 
doi:10.1182/blood-2014-05-577270 pmid:25320243 pmcid:PMC4347284 fatcat:jdw5si5igndhndb22nxblz3day

Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells

Filippo Zambelli, Joke Mertens, Dominika Dziedzicka, Johan Sterckx, Christina Markouli, Alexander Keller, Philippe Tropel, Laura Jung, Stephane Viville, Hilde Van de Velde, Mieke Geens, Sara Seneca (+2 others)
2018 Stem Cell Reports  
ACKNOWLEDGMENTS The authors would like to acknowledge Lise Barbé for providing DNA samples from the VUBi004 lines.  ...  The samples are hybridized on the microarray slide (4 3 44K Human Genome CGH Microarray, Agilent Technologies) for 24 hr.  ...  The data were extracted using Agilent Feature Extraction software and analyzed with the ''ArrayCGHbase'' analysis platform (http://medgen.ugent.be/arrayCGHbasecmgg/) (Menten et al., 2005) .  ... 
doi:10.1016/j.stemcr.2018.05.007 pmid:29910126 pmcid:PMC6117474 fatcat:kw2tp33wuberlnumet74gxsm2q

A Novel t(8;14)(q24;q11) Rearranged Human Cell Line as a Model for Mechanistic and Drug Discovery Studies of NOTCH1-Independent Human T-Cell Leukemia

Valeria Tosello, Gloria Milani, Annalisa Martines, Nadia Macri, Wouder Van Loocke, Filip Matthijssens, Barbara Buldini, Sonia Minuzzo, Deborah Bongiovanni, Richard Fabian Schumacher, Alberto Amadori, Pieter Van Vlierberghe (+1 others)
2018 Cells  
Altogether, this cell line may be a useful model system for dissecting the signaling pathways implicated in NOTCH1-independent T-ALL and for the screening of targeted anti-leukemia agents specific for  ...  Identification of drug targets and mechanistic insights for this disease are still limited.  ...  Scarparo for performing immunophenotypic analysis of cell lines and xenografts.  ... 
doi:10.3390/cells7100160 pmid:30304769 pmcid:PMC6209910 fatcat:bcvvsgafpvevxi3tjs6lwl3lza

PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia

Ingrid M Ariës, Kimberly Bodaar, Salmaan A Karim, Triona Ni Chonghaile, Laura Hinze, Melissa A Burns, Maren Pfirrmann, James Degar, Jack T Landrigan, Sebastian Balbach, Sofie Peirs, Björn Menten (+18 others)
2018 Journal of Experimental Medicine  
We thank Aaron Thorner, Paul Van Hummelen, and Matthew Ducar for assistance with targeted exome sequencing analysis.  ...  We thank Jian Xu for SUZ12 shRNA hairpins, Tobias Neff and Scott Armstrong for Ezh2and Eed-floxed mice, Dario Altieri for gamitrinib, and Andrew Weng and David Weinstock for some of the patient-derived  ...  To investigate underlying mechanisms, we began by applying targeted exome sequencing, array comparative genomic hybridization (CGH), and RNA sequencing analysis (RNA-seq) to all cases with sufficient available  ... 
doi:10.1084/jem.20180570 pmid:30404791 pmcid:PMC6279404 fatcat:qqjbjxt7nbd5vhdp2to5zsxnai